Gen. Efrain Rios Montt, who came to power in a military coup 16 months ago with what he said was a mandate from God, was overthrown today by the Guatemalan officer corps in a swift showdown that left one soldier dead and several wounded.

The defense minister, Gen. Oscar Humberto Mejia Victores, 52, was quickly sworn in as chief of state in a ceremony attended by the country's regional Army commanders to demonstrate solidarity with the coup d'etat. Most of Rios Montt's former Cabinet also attended the swearing-in, officiated by Supreme Court President Ricardo Sagastume Vidaurre.

Mejia asserted in an informal news conference that Rios Montt, 57, has been relegated to "military availability," a Guatemalan military status roughly equivalent to being pensioned.

This indicated that the toppled president was still alive, but his whereabouts were unknown, and nothing was heard from him. After a brief flurry of gunfire from loyal presidential guards this morning during which Air Force jets buzzed his palace, however, there was no sign that any military units opposed his replacement. The capital was calm tonight.

Mejia pledged to retain friendly relations with the United States and said the Army's "struggle by all means against Marxist-Leninist subversion" will continue unabated. This was a reference to leftist guerrillas fighting a back-country war that Rios Montt's often ruthless methods have reduced to isolated skirmishes during the past year.

In Washington, a State Department spokesman said, "We understand Gen. Mejia has pledged to assist the process of democratization and pluralism. While at this point we have no official comment to offer regarding the nature of relations we might have with the new regime, we would welcome any concrete steps to set up an orderly process for a return to democratic rule."

Mejia's takeover seemed to usher in a new period of uncertainty for Washington after Rios Montt's reliable if eccentric stewardship in the ornate Guatemalan presidential palace.

President Reagan, responding to complaints about Guatemalan human rights abuses, said last December after a meeting with Rios Montt that the then-president had received "a bum rap" and his administration moved toward resumption of U.S. military aid. The administration has proposed a modest amount of military assistance in its current budget in recognition of what it sees as progress toward improved human rights and democracy, but there is still strong opposition in the House of Representatives to military aid to Guatemala.

Four Republican members of the House Foreign Affairs Committee met with Mejia Feb. 21-22 in Guatemala, shortly after the disappearance of a Guatemalan anthropologist who was working for the U.S. Agency for International Development and who later turned up dead. According to a staff member interviewed in Washington, the four "were uncomfortable with Mejia's apparent unwillingness to take the human rights concerns of the Congress seriously." The four tried to impress the need to consider those worries, the staffer said, but Mejia "didn't seem to be particularly interested."

Mejia, with more than 30 years of military service behind him, is known as a fervent anticommunist and a frequently outspoken interlocutor in contacts with foreign diplomats and other officials. According to Guatemalan press accounts, he had what amounted to a shouting match with Rep. Clarence D. Long (D-Md.), chairman of a key subcommittee for aid legislation who has opposed aid to Guatemala pending resolution of human rights issues, early this year during one of Long's visits to Central America.

The paunchy Mejia, wearing a khaki uniform and tinted aviator glasses, pledged in a communique read out at 10:30 a.m. that Rios Montt's controversial secret military tribunals that led to 15 executions will be abolished Tuesday. A "state of alarm" imposed by Rios Montt during a coup threat June 29 also will be lifted, he added, and elections for president will be held according to a calendar announced previously.

Rios Montt announced during the June coup threat that an assembly will be chosen next year to write a constitution. But he never said when presidential elections would be held, and informed sources here said then that he had 1985 in mind, with a new president taking power only in 1986.

Despite the vagueness on elections, abolishing the secret tribunals and lifting the state of alarm restrictions were likely to be seen by Guatemalans as steps toward liberalization compared with Rios Montt's rule, if they are carried out as announced.

"In the name of and representing the Guatemalan Army, interpreting the institutional feeling, with unshakable faith in the destiny of the fatherland, without personal ambitions of any kind, as a professional soldier, forged in service of my country, I have accepted with humility, serenity and determination the responsibility that today it befalls me to direct the destinies of the nation," Mejia said at his swearing-in.

The general specifically said that he does not consider himself president. This indicated that he views his role, for the moment at least, as a representative of the officer corps administering the country until a new government can be elected.

"I am not the president because I consider the president is elected by the people," he said, adding later: "I will turn over power only to an elected president."

Observers recalled that Rios Montt also portrayed himself as a temporary leader setting out to prepare the country for early elections of a civilian president when he took power following a coup by young officers March 23, 1982.

Some residents here warned that Mejia's takeover, even though it appeared to be a temporary custodianship in the name of the officer corps, could "awaken ambition" among other officers or in Mejia himself. Their comments reflected fears that Mejia could try to remain in power or that his fellow officers, having seen another coup, could try to take command and wield power themselves.

"In a matter of 30 days we'll see another change in Guatemala," predicted one Guatemalan former official living outside the country who closely follows events in his homeland.

Mejia's communique indicated that Rios Montt's religious zeal as an elder of the fundamentalist Church of the Word played a strong role in dissatisfaction leading to today's coup. In a clear reference to Rios Montt's religious advisers, it complained of "a narrow group that for personal ambitions sought . . . to perpetuate itself in power."

"We have found it to be true that an aggressive and fanatic religious group, benefiting from positions of power held by its highest members, has used and abused the means of the government for its own benefit, ignoring the fundamental principle of separation of church and state," it said.

This was interpreted as a reference to Sergio Contreras Valladeres and Francisco Bianchi, two church elders who were among Rios Montt's closest advisers with offices adjoining his in the presidential palace. Their whereabouts also were unknown.

Their removal was one of the key demands put forth by Army officers during the June 29 tension that brought Rios Montt to the brink of a coup.

According to reports from political figures here at the time, Rios Montt had pledged to dismiss them during his negotiations with military officers to avoid being dismissed from the presidency. But sources said they were still serving when today's coup d'etat was carried out.

Tension also had been rising among businessmen and urban groups over a variation of a value-added tax that went into effect Aug. 1. Mejia said parts of the project would be reexamined. But its architect, Finance Minister Leonardo Figueroa Villarde, remained in the Cabinet for the time being, and it was not clear whether the levy would be lifted.

Guatemalan political leaders also had voiced complaints at Rios Montt's unwillingness to set a specific date for presidential elections. They voiced suspicion that he considered his "messianic" mission so essential to the country that he would be reluctant to relinquish power despite his pledges.

Mejia emphasized, however, that the nation's politicians played no part in pushing Rios Montt from office. "There was no political participation in the coup," he said.

Diplomatic sources said that despite the long list of complaints against Rios Montt it was unclear what specifically precipitated the coup today. Sources with frequent access to Guatemalan officers said they were caught by surprise when it became apparent this morning that the officer corps was rising up against Rios Montt.